Make NanoStat module recognize more report flavors #1594
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Use the string "General summary:" followed by 9 spaces in the first line to distinguish a NanoStat report. Those 9 spaces probably aren't supposed to be there, but they are found in all of the test files, and Linus says it's a feature and not a bug once people start depending on it. Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
The [NanoStat source code](https://github.com/wdecoster/nanostat/blob/f50c7530f072e9e2b3c830334d806a619dc37c68/nanostat/NanoStat.py#L42-L55) reveals that the number of space characters after the first line is actually variable based upon the output of the next few lines. Update the search pattern with a regular expression that can handle such variability. Fixes: 38899d7 (Update NanoStat search pattern) Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
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Looking through the CI logs, it looks like different flavors of NanoStat report cannot be parsed within the same run using the current logic. I will look into workarounds for that. |
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
ewels
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Check that we can handle bad files as search pattern is quite general now. See MultiQC/MultiQC#1594
ewels
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Jan 15, 2022
vladsavelyev
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Apr 16, 2022
Check that we can handle bad files as search pattern is quite general now. See MultiQC/MultiQC#1594
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CHANGELOG.mdhas been updatedAs noted in #1547, the NanoStat module is currently ignoring NanoStat reports generated from fasta and fastq files. Fix that by
I have tested this PR with every test file contained in MultiQC/test-data#221, and received output from every file.